Merge pull request ANTsX#535 from ANTsX/ITKv5

ITKv5 preparation
gandreadis · Feb 13, 2018 · 30eabeb · 30eabeb
2 parents c95e77a + 477cf4c
commit 30eabeb
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Showing 75 changed files with 226 additions and 215 deletions.
diff --git a/ANTS.cmake b/ANTS.cmake
@@ -68,7 +68,7 @@ if(USE_VTK)
    vtkImagingGeneral
    vtkRenderingAnnotation
    )
-  else(VTK_VERSION_MAJOR GREATER 6)
+  else()
      find_package(VTK COMPONENTS vtkRenderingVolumeOpenGL
      vtkCommonCore
      vtkCommonDataModel
@@ -80,16 +80,16 @@ if(USE_VTK)
      vtkImagingStencil
      vtkImagingGeneral
      vtkRenderingAnnotation)
-  endif(VTK_VERSION_MAJOR GREATER 6)
+  endif()
 
   if(VTK_FOUND)
     include(${VTK_USE_FILE})
     include_directories(${VTK_INCLUDE_DIRS})
     set(INIT_VTK_LIBRARIES ${VTK_LIBRARIES})
-  else(VTK_FOUND)
+  else()
      message("Cannot build some programs without VTK.  Please set VTK_DIR if you need these programs.")
-  endif(VTK_FOUND)
-endif(USE_VTK)
+  endif()
+endif()
 
 # With MS compilers on Win64, we need the /bigobj switch, else generated
 # code results in objects with number of sections exceeding object file
@@ -106,11 +106,11 @@ if (ITK_USE_FFTWD OR ITK_USE_FFTWF)
   if(ITK_USE_SYSTEM_FFTW)
       find_package( FFTW )
       link_directories(${FFTW_LIBDIR})
-  else(ITK_USE_SYSTEM_FFTW)
+  else()
       link_directories(${ITK_DIR}/fftw/lib)
       include_directories(${ITK_DIR}/fftw/include)
-  endif(ITK_USE_SYSTEM_FFTW)
-endif(ITK_USE_FFTWD OR ITK_USE_FFTWF)
+  endif()
+endif()
 
 # These are configure time options that specify which
 # subset of tests should be run

diff --git a/CMake/ProjectSourceVersion.cmake b/CMake/ProjectSourceVersion.cmake
@@ -106,7 +106,7 @@ if(_GIT_VERSION VERSION_EQUAL _${CMAKE_PROJECT_NAME}_VERSION)
 else()
   # The first commit after a tag should increase the project version
   # number in Version.cmake and be "dev1"
-  MATH(EXPR _GIT_VERSION_COUNT "${_GIT_VERSION_COUNT}+1")
+  math(EXPR _GIT_VERSION_COUNT "${_GIT_VERSION_COUNT}+1")
   set(_GIT_VERSION_DEV "${_GIT_VERSION_COUNT}")
 endif()
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,16 +1,27 @@
-cmake_minimum_required(VERSION 2.8.9)
-cmake_policy(VERSION 2.8.9)
+if(CMAKE_CXX_STANDARD)
+  #if CMAKE_CXX_STANDARD is requested, then require
+  #new version of cmake to force C++11 that can
+  #improve support of C++11 features.
+  cmake_minimum_required(VERSION 3.8.2 FATAL_ERROR)
+else()
+  cmake_minimum_required(VERSION 2.8.9)
+  cmake_policy(VERSION 2.8.9)
+endif()
 
-find_program(CCACHE_PROGRAM ccache)
-if(CCACHE_PROGRAM)
+option(ANTS_BUILD_WITH_CCACHE "Build ${LOCAL_PROJECT_NAME} using ccache if available." ON)
+mark_as_advanced(ANTS_BUILD_WITH_CCACHE)
+if(ANTS_BUILD_WITH_CCACHE)
+  find_program(CCACHE_PROGRAM ccache)
+  if(CCACHE_PROGRAM)
     set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${CCACHE_PROGRAM}")
+  endif()
 endif()
 
 set(LIBRARY_SOVERSION_INFO 2)
 set(LIBRARY_VERSION_INFO 2.2.0)
 
 set(LOCAL_PROJECT_NAME ANTS)
-INCLUDE(InstallRequiredSystemLibraries)
+include(InstallRequiredSystemLibraries)
 ## NOTE THERE SHOULD BE NO PROJECT STATEMENT HERE!
 ## This file acts as a simple switch to initiate
 ## two completely independant CMake build environments.

diff --git a/Common.cmake b/Common.cmake
@@ -25,14 +25,14 @@ set(ANTS_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
 
 ######################################################################################################
 # BA - add this stuff to help installation of ANTsR
-# SET(CMAKE_SKIP_BUILD_RPATH  FALSE)
-# SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-# SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-# SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-# LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
-# IF("${isSystemDir}" STREQUAL "-1")
-#   SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-# ENDIF("${isSystemDir}" STREQUAL "-1")
+# set(CMAKE_SKIP_BUILD_RPATH  FALSE)
+# set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+# set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+# set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+# list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+# if("${isSystemDir}" STREQUAL "-1")
+#   set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+# endif("${isSystemDir}" STREQUAL "-1")
 #####################################################################################################
 
 set(USE_ITKv4 ON)

diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
@@ -25,7 +25,7 @@ macro(STANDARD_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
   set( ANTS_FUNCTION_NAME ${ANTS_FUNCTION_NAME} )
 
   add_library(l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}.cxx)
-  SET_TARGET_PROPERTIES(l_${ANTS_FUNCTION_NAME} PROPERTIES
+  set_target_properties(l_${ANTS_FUNCTION_NAME} PROPERTIES
     SOVERSION ${LIBRARY_SOVERSION_INFO}  VERSION ${LIBRARY_VERSION_INFO})
   message(STATUS "${ANTS_FUNCTION_NAME} ${EXTRA_LIBS}")
   target_link_libraries(l_${ANTS_FUNCTION_NAME} antsUtilities ${EXTRA_LIBS} )
@@ -160,13 +160,13 @@ if (BUILD_ALL_ANTS_APPS)
   foreach(ANTS_APP ${MORE_ANTS_APPS})
     STANDARD_ANTS_BUILD(${ANTS_APP} "")
   endforeach()
-else(BUILD_ALL_ANTS_APPS)
+else()
   foreach(ANTS_APP ${MORE_ANTS_APPS})
     if(ANTS_BUILD_${ANTS_APP})
       STANDARD_ANTS_BUILD(${ANTS_APP} "")
     endif()
   endforeach()
-endif(BUILD_ALL_ANTS_APPS)
+endif()
 
 
 if(USE_VTK)
@@ -185,7 +185,7 @@ set(VTK_ANTS_APPS
 foreach(ANTS_APP ${VTK_ANTS_APPS})
   STANDARD_ANTS_BUILD(${ANTS_APP} "${VTK_LIBRARIES}")
 endforeach()
-endif(USE_VTK)
+endif()
 
 install(PROGRAMS ../Scripts/ANTSpexec.sh
      ../Scripts/antsASLProcessing.sh
@@ -220,18 +220,18 @@ if( COPY_SCRIPT_FILES_TO_BIN_DIR )
   file( GLOB PSCRIPT_FILES "../Scripts/*.pl" )
   foreach( SCRIPT_FILE ${SCRIPT_FILES} )
     message( "  Copying ${SCRIPT_FILE} to ${CMAKE_CURRENT_BINARY_DIR}/../../bin/" )
-    CONFIGURE_FILE( ${SCRIPT_FILE} ${CMAKE_CURRENT_BINARY_DIR}/../../bin/ COPYONLY )
-  endforeach( SCRIPT_FILE )
+    configure_file( ${SCRIPT_FILE} ${CMAKE_CURRENT_BINARY_DIR}/../../bin/ COPYONLY )
+  endforeach()
   foreach( SCRIPT_FILE ${PSCRIPT_FILES} )
     message( "  Copying ${SCRIPT_FILE} to ${CMAKE_CURRENT_BINARY_DIR}/../../bin/" )
-    CONFIGURE_FILE( ${SCRIPT_FILE} ${CMAKE_CURRENT_BINARY_DIR}/../../bin/ COPYONLY )
-  endforeach( SCRIPT_FILE )
-endif( COPY_SCRIPT_FILES_TO_BIN_DIR )
+    configure_file( ${SCRIPT_FILE} ${CMAKE_CURRENT_BINARY_DIR}/../../bin/ COPYONLY )
+  endforeach()
+endif()
 
 ## Build test option
 if(BUILD_TESTING)
     add_subdirectory(TestSuite)
-endif(BUILD_TESTING)
+endif()
 
 set(CPACK_PACKAGE_NAME "ANTs")
 set(CPACK_PACKAGE_VENDOR "CMake.org")

diff --git a/Examples/TestSuite/CMakeLists.txt b/Examples/TestSuite/CMakeLists.txt
@@ -29,7 +29,7 @@ macro(MakeTestDriverFromANTSbinary ANTSbinaryName ANTSbinaryTestSourceName ANTS_
     LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
     ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
     )
-endmacro(MakeTestDriverFromANTSbinary ANTSbinaryName)
+endmacro()
 
 #-----------------------------------------------------------------------
 # Setup locations to find externally maintained test data.
@@ -949,7 +949,7 @@ endif()
 
 ############ End of CompositeTransformUtil tests#################
 
-endif(RUN_LONG_TESTS)
+endif()
 
 ##############################################################
 ##############################################################
@@ -1075,11 +1075,11 @@ ExternalData_expand_arguments(${PROJECT_NAME}FetchData C_IMAGE DATA{${SMALL_DATA
 
 include(ANTS_SYN_WITH_TIME_test.cmake)
 include(APOC_OTSU_INIT_test.cmake)
-endif(RUN_LONG_TESTS)
+endif()
 
 include(ANTS_PSE_MSQ_TXT_test.cmake)
 include(ANTS_PSE_MSQ_VTK_test.cmake)
 
-endif(RUN_SHORT_TESTS)
+endif()
 
 ExternalData_add_target( ${PROJECT_NAME}FetchData )  # Name of data management target
diff --git a/Examples/itkantsRegistrationHelper.h b/Examples/itkantsRegistrationHelper.h
@@ -792,7 +792,7 @@ class RegistrationHelper : public itk::Object
 
 protected:
   RegistrationHelper();
-  virtual ~RegistrationHelper();
+  virtual ~RegistrationHelper() ITK_OVERRIDE;
 private:
 
   typename itk::ImageBase<VImageDimension>::Pointer GetShrinkImageOutputInformation(const itk::ImageBase<VImageDimension> * inputImageInformation,

diff --git a/ImageRegistration/itkANTSAffine3DTransform.h b/ImageRegistration/itkANTSAffine3DTransform.h
@@ -99,7 +99,7 @@ class ANTSAffine3DTransform :
   itkGetConstReferenceMacro( K3, TScalarType );
 
   /** Set the parameters to the IdentityTransform */
-  virtual void SetIdentity() ITK_OVERRIDE;
+  void SetIdentity() ITK_OVERRIDE;
 
   /** Set the transformation from a container of parameters.
    * This is typically used by optimizers.
@@ -126,20 +126,20 @@ class ANTSAffine3DTransform :
  * Get local Jacobian for the given point
  * \c j will sized properly as needed.
  */
-  virtual void ComputeJacobianWithRespectToParameters(const InputPointType  & p, JacobianType & j) const ITK_OVERRIDE;
+  void ComputeJacobianWithRespectToParameters(const InputPointType  & p, JacobianType & j) const ITK_OVERRIDE;
 
 protected:
 /*   ANTSAffine3DTransform(const MatrixType &matrix, */
 /*                            const OutputVectorType &offset); */
   ANTSAffine3DTransform(unsigned int outputDims, unsigned int paramDims);
   ANTSAffine3DTransform();
-  ~ANTSAffine3DTransform()
+  virtual ~ANTSAffine3DTransform() ITK_OVERRIDE
   {
   };
 
-  virtual void ComputeMatrix() ITK_OVERRIDE;
+  void ComputeMatrix() ITK_OVERRIDE;
 
-  virtual void ComputeMatrixParameters() ITK_OVERRIDE;
+  void ComputeMatrixParameters() ITK_OVERRIDE;
 
   void SetVarRotation(const VnlQuaternionType & rotation)
   {

diff --git a/ImageRegistration/itkANTSCenteredAffine2DTransform.h b/ImageRegistration/itkANTSCenteredAffine2DTransform.h
@@ -174,7 +174,7 @@ class ANTSCenteredAffine2DTransform :
    * Get local Jacobian for the given point
    * \c j will sized properly as needed.
    */
-  virtual void ComputeJacobianWithRespectToParameters(const InputPointType  & p, JacobianType & j) const ITK_OVERRIDE;
+  void ComputeJacobianWithRespectToParameters(const InputPointType  & p, JacobianType & j) const ITK_OVERRIDE;
 
   /**
    * This method creates and returns a new ANTSCenteredAffine2DTransform object
@@ -189,7 +189,7 @@ class ANTSCenteredAffine2DTransform :
   void CloneTo( Pointer & clone ) const;
 
   /** Reset the parameters to create and identity transform. */
-  virtual void SetIdentity() ITK_OVERRIDE;
+  void SetIdentity() ITK_OVERRIDE;
 
 protected:
   // Rigid2DTransform();
@@ -200,7 +200,7 @@ class ANTSCenteredAffine2DTransform :
   ANTSCenteredAffine2DTransform( unsigned int outputSpaceDimension, unsigned int parametersDimension);
 
   //  ~Rigid2DTransform();
-  ~ANTSCenteredAffine2DTransform();
+  virtual ~ANTSCenteredAffine2DTransform() ITK_OVERRIDE;
 
   /**
     * Print contents of an ANTSCenteredAffine2DTransform
@@ -210,13 +210,13 @@ class ANTSCenteredAffine2DTransform :
   /** Compute the matrix from angle. This is used in Set methods
    * to update the underlying matrix whenever a transform parameter
    * is changed. */
-  virtual void ComputeMatrix() ITK_OVERRIDE;
+  void ComputeMatrix() ITK_OVERRIDE;
 
   /** Compute the angle from the matrix. This is used to compute
    * transform parameters from a given matrix. This is used in
    * MatrixOffsetTransformBase::Compose() and
    * MatrixOffsetTransformBase::GetInverse(). */
-  virtual void ComputeMatrixParameters() ITK_OVERRIDE;
+  void ComputeMatrixParameters() ITK_OVERRIDE;
 
   /** Update angle without recomputation of other internal variables. */
   void SetVarAngle( TScalarType angle )

diff --git a/ImageRegistration/itkANTSImageRegistrationOptimizer.h b/ImageRegistration/itkANTSImageRegistrationOptimizer.h
@@ -2091,7 +2091,7 @@ class ANTSImageRegistrationOptimizer
   }
 
   ANTSImageRegistrationOptimizer();
-  virtual ~ANTSImageRegistrationOptimizer()
+  virtual ~ANTSImageRegistrationOptimizer() ITK_OVERRIDE
   {
   }
 

diff --git a/ImageRegistration/itkANTSImageTransformation.h b/ImageRegistration/itkANTSImageTransformation.h
@@ -165,7 +165,7 @@ class ANTSImageTransformation
   itkBooleanMacro( WriteComponentImages );
 protected:
   ANTSImageTransformation();
-  virtual ~ANTSImageTransformation()
+  virtual ~ANTSImageTransformation() ITK_OVERRIDE
   {
   }
 

diff --git a/ImageRegistration/itkAvantsMutualInformationRegistrationFunction.h b/ImageRegistration/itkAvantsMutualInformationRegistrationFunction.h
@@ -194,14 +194,14 @@ class AvantsMutualInformationRegistrationFunction :
   }
 
   /** This class uses a constant timestep of 1. */
-  virtual TimeStepType ComputeGlobalTimeStep(void *itkNotUsed(GlobalData) ) const ITK_OVERRIDE
+  TimeStepType ComputeGlobalTimeStep(void *itkNotUsed(GlobalData) ) const ITK_OVERRIDE
   {
     return 1;
   }
 
   /** Return a pointer to a global data structure that is passed to
    * this object from the solver at each calculation.  */
-  virtual void * GetGlobalDataPointer() const ITK_OVERRIDE
+  void * GetGlobalDataPointer() const ITK_OVERRIDE
   {
     GlobalDataStruct *global = new GlobalDataStruct();
 
@@ -212,13 +212,13 @@ class AvantsMutualInformationRegistrationFunction :
   }
 
   /** Release memory for global data structure. */
-  virtual void ReleaseGlobalDataPointer( void *GlobalData ) const ITK_OVERRIDE
+  void ReleaseGlobalDataPointer( void *GlobalData ) const ITK_OVERRIDE
   {
     delete (GlobalDataStruct *) GlobalData;
   }
 
   /** Set the object's state before each iteration. */
-  virtual void InitializeIteration() ITK_OVERRIDE;
+  void InitializeIteration() ITK_OVERRIDE;
 
   typedef double CoordinateRepresentationType;
 
@@ -494,7 +494,7 @@ class AvantsMutualInformationRegistrationFunction :
     return this->m_Energy;
   }
 
-  virtual VectorType ComputeUpdateInv(const NeighborhoodType & neighborhood,
+  VectorType ComputeUpdateInv(const NeighborhoodType & neighborhood,
                                       void * /* globalData */,
                                       const FloatOffsetType & /* offset */ = FloatOffsetType(0.0) ) ITK_OVERRIDE
   {
@@ -584,7 +584,7 @@ class AvantsMutualInformationRegistrationFunction :
     return (double) this->m_Padding + windowTerm * (float)(this->m_NumberOfHistogramBins - this->m_Padding);
   }
 
-  virtual VectorType ComputeUpdate(const NeighborhoodType & neighborhood,
+  VectorType ComputeUpdate(const NeighborhoodType & neighborhood,
                                    void * /* globalData */,
                                    const FloatOffsetType & /* offset */ = FloatOffsetType(0.0) ) ITK_OVERRIDE
   {
@@ -688,7 +688,7 @@ class AvantsMutualInformationRegistrationFunction :
 protected:
 
   AvantsMutualInformationRegistrationFunction();
-  virtual ~AvantsMutualInformationRegistrationFunction()
+  virtual ~AvantsMutualInformationRegistrationFunction() ITK_OVERRIDE
   {
   };
   void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;

diff --git a/ImageRegistration/itkAvantsPDEDeformableRegistrationFunction.h b/ImageRegistration/itkAvantsPDEDeformableRegistrationFunction.h
@@ -224,7 +224,7 @@ class AvantsPDEDeformableRegistrationFunction :
     return update * this->m_GradientStep;
   }
 
-  virtual VectorType ComputeUpdate(const NeighborhoodType & neighborhood,
+  VectorType ComputeUpdate(const NeighborhoodType & neighborhood,
                                    void * /* globalData */,
                                    const FloatOffsetType & /* offset */ = FloatOffsetType(0.0) ) ITK_OVERRIDE
   {
@@ -318,7 +318,7 @@ class AvantsPDEDeformableRegistrationFunction :
     this->m_RobustnessParameter = -1.e12;
   }
 
-  ~AvantsPDEDeformableRegistrationFunction()
+  virtual ~AvantsPDEDeformableRegistrationFunction() ITK_OVERRIDE
   {
   }
-Original file line number
+Diff line change
@@ Expand Up / @@ -2091,7 +2091,7 @@ class ANTSImageRegistrationOptimizer @@
       }
       ANTSImageRegistrationOptimizer();
-      virtual ~ANTSImageRegistrationOptimizer()
+      virtual ~ANTSImageRegistrationOptimizer() ITK_OVERRIDE
       {
       }
@@ Expand Down @@